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Biomedical subjects

Kristina Nilsson

Publications and source records attributed to Kristina Nilsson.

15 recordsLinked to original sources
PubMed2006

Subcellular localization, modification and protein complex formation of the cdk-inhibitor p16 in Rb-functional and Rb-inactivated tumor cells.

The cdk-inhibitor p16 is a tumor suppressor gene that is inactivated in many forms of cancer. Despite numerous studies, the exact mechanism of regulation of p16 has not been clarified, although the status of retinoblastoma (Rb) seems to be one important factor that influences the p16 expression. The specificity and validity of cytoplasmic localization of p16 observed in some tumors has further been questioned. Here, by subcellular fractionation of Rb-functional and Rb-inactivated cell lines, we show that p16 indeed is expressed in the cytoplasm as well as in the nucleus. Post translational modifications of p16 in different subcellular compartments as well as its capacity to form protein complexes were further delineated. Two dimensional gel electrophoresis showed that two forms of p16 appeared in the cytoplasm, while only one form was detected in the nucleus. Samples of basal cell carcinoma and squamous cell carcinoma of the skin with either functional or non-functional Rb also exhibited at least two forms of p16. In addition, cytoplasmic p16 bound cyclin dependent kinase (cdk)4/6, potentially indicating that p16 could have a function in the cytoplasm.

Cell Line, Tumor↗
PubMed2005

Cyclin I is expressed in human breast cancer and closely associated with VEGF and KDR expression.

In the present study, cyclin I protein expression in 114 invasive human breast cancers was correlated with cell cycle and angiogenesis-related proteins and clinico-pathological data. A strong association was found between cytoplasmic cyclin I staining and VEGF (p = 0.001) as well as the VEGF receptor KDR (p = 0.001), suggesting a link between cyclin I and angiogenesis.

Amino Acid Sequence↗
PubMed2005

Diseases and mortality in free-ranging brown bear (Ursus arctos), gray wolf (Canis lupus), and wolverine (Gulo gulo) in Sweden.

Ninety-eight brown bears (Ursus arctos), 20 gray wolves (Canis lupus), and 27 wolverines (Gulo gulo), all free-ranging, were submitted to the National Veterinary Institute, Uppsala, Sweden, during 1987-2001 for investigation of diseases and causes of mortality. The most common cause of natural death in brown bears was infanticide. Infanticide also was observed in wolverines but not in wolves. Traumatic injuries, originating from road or railway accidents, were the most common cause of death in wolves and occurred occasionally in brown bears. Most wolverines were submitted as forensic cases in which illegal hunting/poaching was suspected. Sarcoptic mange was observed in several wolves but not in brown bears or wolverines. Sarcoptic mange most likely was acquired from infected red foxes (Vulpes vulpes) that were killed by wolves. Other parasites and infectious diseases were only found sporadically.

Animal Diseases↗
PubMed2004

The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: quantum refinement.

Treatment of met-myoglobin (FeIII) with H2O2 gives rise to ferryl myoglobin, which is closely related to compound II in peroxidases. Experimental studies have given conflicting results for this species. In particular, crystallographic and extended x-ray absorption fine-structure data have shown either a short (approximately 170 pm) or a longer (approximately 190 pm) Fe-O bond, indicating either a double or a single bond. We here present a combined experimental and theoretical investigation of this species. In particular, we use quantum refinement to re-refine a crystal structure with a long bond, using 12 possible states of the active site. The states differ in the formal oxidation state of the iron ion and in the protonation of the oxygen ligand (O2-, OH-, or H2O) and the distal histidine residue (with a proton on Ndelta1, Nepsilon2, or on both atoms). Quantum refinement is essentially standard crystallographic refinement, where the molecular-mechanics potential, normally used to supplement the experimental data, is replaced by a quantum chemical calculation. Thereby, we obtain an accurate description of the active site in all the different protonation and oxidation states, and we can determine which of the 12 structures fit the experimental data best by comparing the crystallographic R-factors, electron-density maps, strain energies, and deviation from the ideal structure. The results indicate that FeIII OH- and FeIV OH- fit the experimental data almost equally well. These two states are appreciably better than the standard model of compound II, FeIV O2-. Combined with the available spectroscopic data, this indicates that compound II in myoglobin is protonated and is best described as FeIV OH-. It accepts a hydrogen bond from the distal His, which may be protonated at low pH.

Binding Sites↗
PubMed2004

Protonation status of metal-bound ligands can be determined by quantum refinement.

The protonation status of key residues and bound ligands are often important for the function of a protein. Unfortunately, protons are not discerned in normal protein crystal structures, so their positions have to be determined by more indirect methods. We show that the recently developed quantum refinement method can be used to determine the position of protons in crystal structures. By replacing the molecular-mechanics potential, normally used in crystallographic refinement, by more accurate quantum chemical calculations, we get information about the ideal structure of a certain protonation state. By comparing the refined structures of different protonation states, the one that fits the crystallographic raw data best can be decided using four criteria: the R factors, electron density maps, strain energy, and divergence from the unrestrained quantum chemical structure. We test this method on alcohol dehydrogenase, for which the pK(a) of the zinc-bound solvent molecule is experimentally known. We show that we can predict the correct protonation state for both a deprotonated alcohol and a neutral water molecule.

Alcohol Dehydrogenase↗
PubMed2004

Retinoblastoma protein function and p16INK4a expression in actinic keratosis, squamous cell carcinoma in situ and invasive squamous cell carcinoma of the skin and links between p16INK4a expression and infiltrative behavior.

p16INK4a is involved in many important regulatory events in the cell and the expression and function is closely associated with the retinoblastoma protein (Rb). Earlier, we have in colorectal cancer and in basal cell carcinoma showed that p16INK4a is upregulated at the invasive front causing cell cycle arrest in infiltrative tumor cells via a functional Rb. This role for p16INK4a as a regulator of proliferation when tumor cells infiltrate might besides a general cyclin-dependent kinase (cdk) inhibitory effect explain why p16INK4a is deregulated in many tumor forms. The expression pattern of p16INK4a in relation to Rb-function in squamous cancer and precancerous forms of the skin has not been fully detailed. We therefore characterized the expression of p16INK4a, Rb-phosphorylation and proliferation in actinic keratosis, squamous cell carcinoma in situ and invasive squamous cell carcinoma with special reference to infiltrative behavior. The expression of p16INK4a varied between the lesions, with weak and cytoplasmic p16INK4a expression and functional Rb in actinic keratosis. Strong nuclear and cytoplasmic p16INK4a expression was observed in all carcinomas in situ in parallel with lack of Rb-phosphorylation but high proliferation indicating a nonfunctional Rb. Invasive squamous carcinoma showed a mixed p16INK4a expression pattern where some tumors had strong cytoplasmic p16INK4a expression, large fraction of Rb-phosphorylated cells and high proliferation. Interestingly, despite this disability of p16INK4a to inhibit proliferation there was an upregulation of cytoplasmic p16INK4a in infiltrative cells compared to tumor cells towards the tumor center. A similar scenario but strong and combined nuclear and cytoplasmic p16INK4a expression in infiltrative cells, was observed in other invasive squamous cancers. This suggests that the p16INK4a upregulation in infiltrative cells is governed independently of the subcellular localization or of the potential to affect proliferation via Rb, and suggests a potentially proliferation independent function for p16INK4a in infiltrative behavior.

Blotting, Western↗
PubMed2004

Investigations into shaking mink syndrome: an encephalomyelitis of unknown cause in farmed mink (Mustela vison) kits in Scandinavia.

An apparently novel neurological disease clinically characterized by shaking, tremors, seizures, staggering gait, and ataxia was first observed in farmed mink kits in Denmark in 2000 and subsequently in Sweden, Denmark, and Finland in 2001, and again in Denmark in 2002. Lymphoplasmacytic encephalomyelitis was found in the affected kits. The lesions were most severe in the brainstem and cerebellum and consisted of neuronal degeneration and necrosis, neuronophagia, focal and diffuse gliosis, perivascular cuffs formed by lymphocytes, plasma cells and macrophages, and segmental loss of Purkinje cells. Testing was conducted to determine the cause of the disease, including general virological investigations (virus culture, negative-staining electron microscopy, immunoelectron microscopy, polymerase chain reaction for herpesviruses, adenoviruses, pestiviruses, and coronaviruses), tests for specific viral diseases (canine distemper, Borna disease, Louping ill, West Nile virus infection, tick-borne encephalitis, Aleutian disease), tests for protozoa (Toxoplasma gondii, Neospora caninum, Encephalitozoon cuniculi), bacteria (general culture, listeria, Clamydophila psittaci), and intracerebral inoculation of neonatal mice. The results of all these investigations were negative. One group of 3 mink kits inoculated intracerebrally with brain homogenate of affected mink developed clinical signs and histological lesions similar to those observed in naturally infected mink. Based on the histopathological features, it is postulated that the disease is caused by a yet unidentified virus.

Animals↗
PubMed2003

Quantum chemistry can locally improve protein crystal structures.

We have re-refined the X-ray structure of the heme site in cytochrome c553, supplementing the crystallographic data with quantum chemical geometry optimizations, instead of the molecular mechanics force field used in standard crystallographic refinement. By comparing the resulting structure, obtained using medium-resolution data (170 pm), with an atomic-resolution structure (95 pm) of the same protein, we show that the inclusion of quantum chemical information into the refinement procedure improves the structure significantly. Thus, errors in the Fe-ligand distances are reduced from 3 to 32 pm in the low-resolution structure to 0-5 pm in the re-refined structure, one side-chain atom changes its conformation (a movement by 214 pm toward its position in the high-resolution structure), and the R factors are improved by up to 0.018. Thus, quantum refinement may be a powerful method to obtain an accurate structure for interesting parts of a protein.

Crystallography, X-Ray↗
PubMed2003

Invade or proliferate? Two contrasting events in malignant behavior governed by p16(INK4a) and an intact Rb pathway illustrated by a model system of basal cell carcinoma.

Using a highly infiltrative tumor type as basal cell carcinoma as the model system, we have examined the relation between invasive behavior and proliferation. Our results studying alterations in G(1)-S cell cycle regulatory proteins and proliferation in infiltrative cells were surprising and clearly indicated that invasion in tumors with an intact p16(INK4a)-cyclin D-retinoblastoma protein (Rb) pathway was equivalent to ceased proliferation. Using immunohistochemistry and Western blotting of microdissected parts of basal cell carcinomas, we showed that p16(INK4a) was up-regulated at the invasive front of the majority of basal cell carcinomas with infiltrative growth patterns, followed by ceased proliferation, as well as decreased phosphorylation of Rb. Besides supporting the fact that basal cell carcinomas have an intact Rb pathway, our results clearly indicate that invasive tumor cells change phenotype from a proliferative state to an invasive phenotype. Thus, invasion is not necessarily analogous with proliferation, implicating a paradigm shift in the understanding of two central processes in malignant behavior.

Blotting, Western↗
PubMed2003

An automatic method to generate force-field parameters for hetero-compounds.

A program, Hess2FF, has been developed that automatically constructs parameter and topology files to be used in crystallographic refinement for any molecule, based on a Hessian (force-constant) matrix estimated by any method. The program is tested by redefining hetero-compounds in five different proteins: the inhibitor N-methylmesoporphyrin bound to ferrochelatase, the haem group and its axial ligands in cyctochrome c(553), the active-site metal ion in iron superoxide dismutase, the catalytic zinc ion in alcohol dehydrogenase with a bound trifluoroethanol molecule and the 5'-deoxyadenosyl group in methylmalonyl coenzyme A mutase. It is shown that the resulting structures are improved in several aspects. In particular, the free R(free) factor always decreases and it is shown that a 1.70 A structure of cyctochrome c(553) becomes more similar to a high-resolution (0.97 A) structure of the same protein after re-refinement with Hess2FF. Thus, the force field used in crystallographic refinement significantly affects the final structure and therefore should be published together with the structure to ensure reproducibility. Various methods of obtaining the Hessian matrix employed by Hess2FF are discussed and some recommendations are given. Hess2FF allows the user to divide the atoms of the molecule into atom types that share the same force-field parameters. However, it seems to be favourable to assign a separate type to each atom, which can be performed automatically.

Algorithms↗
PubMed2003

Survival in primary lung cancer potentially cured by operation: influence of tumor stage and clinical characteristics.

BACKGROUND: Surgical resection is currently standard treatment in early stage lung cancer. The aim of the present study was to identify stage-related factors and patient characteristics influencing survival after complete resection. METHODS: We identified 395 patients with non-small cell lung cancer who had undergone potentially radical operation during 1987 to 1999 at one thoracic surgery institution in central Sweden. Factors independently related to survival were identified in a multivariate analysis. Survival was analyzed in low-, medium-, and high-risk groups based on a risk score calculated from relative hazards for identified risk factors. RESULTS: Overall 5-year survival among the 395 patients was 51%. The strongest factor predicting prognosis was positive lymph nodes at operation. Higher age, earlier period for operation, impaired lung function, current smoking, and major operative complication were all related to poorer prognosis. Patients with tumor stage Ia had a 5-year survival of 69%, compared to 73% in patients in the low-risk group. CONCLUSIONS: Tumor stage is the best prognostic indicator after radical operation. Inclusion of other tumor- and patient-related variables did not add prognostic information of clinical relevance beyond that provided by tumor stage alone.

Adenocarcinoma↗
PubMed2003

1-methylguanosine-deficient tRNA of Salmonella enterica serovar Typhimurium affects thiamine metabolism.

In Salmonella enterica serovar Typhimurium a mutation in the purF gene encoding the first enzyme in the purine pathway blocks, besides the synthesis of purine, the synthesis of thiamine when glucose is used as the carbon source. On carbon sources other than glucose, a purF mutant does not require thiamine, since the alternative pyrimidine biosynthetic (APB) pathway is activated. This pathway feeds into the purine pathway just after the PurF biosynthetic step and upstream of the intermediate 4-aminoimidazolribotide, which is the common intermediate in purine and thiamine synthesis. The activity of this pathway is also influenced by externally added pantothenate. tRNAs from S. enterica specific for leucine, proline, and arginine contain 1-methylguanosine (m(1)G37) adjacent to and 3' of the anticodon (position 37). The formation of m(1)G37 is catalyzed by the enzyme tRNA(m(1)G37)methyltransferase, which is encoded by the trmD gene. Mutations in this gene, which result in an m(1)G37 deficiency in the tRNA, in a purF mutant mediate PurF-independent thiamine synthesis. This phenotype is specifically dependent on the m(1)G37 deficiency, since several other mutations which also affect translation fidelity and induce slow growth did not cause PurF-independent thiamine synthesis. Some antibiotics that are known to reduce the efficiency of translation also induce PurF-independent thiamine synthesis. We suggest that a slow decoding event at a codon(s) read by a tRNA(s) normally containing m(1)G37 is responsible for the PurF-independent thiamine synthesis and that this event causes a changed flux in the APB pathway.

Anti-Bacterial Agents↗
PubMed2002

Quantum chemical geometry optimizations in proteins using crystallographic raw data.

A method is developed for the combination of quantum chemical geometry optimizations and crystallographic structure refinement. The method is implemented by integrating the quantum chemical software Turbomole with the crystallographic software Crystallography and NMR System (CNS), using three small procedures transferring information between the two programs. The program (COMQUM-X)is used to study the binding of the inhibitor N-methylmesoporphyrin to ferrochelatase, and we show that the method behaves properly and leads to an improvement of the structure of the inhibitor. It allows us to directly quantify in energy terms how much the protein distort the structure of the bound inhibitor compared to the optimum vacuum structure (4-6 kJ/mol). The approach improves the standard combined quantum chemical and molecular mechanics (QC/MM) approach by guaranteeing that the final structure is in accordance with experimental data (the reflections) and avoiding the risk of propagating errors in the crystal coordinates. The program can also be seen as an improvement of standard crystallographic refinement, providing an accurate empirical potential function for any group of interest. The results can be directly interpreted in standard crystallographic terms (e.g., R factors or electron density maps). The method can be used to interpret crystal structures (e.g., the protonation status of metal-bound water molecules) and even to locally improve them.

Binding Sites↗
PubMed2002

The cysteine desulfurase IscS is required for synthesis of all five thiolated nucleosides present in tRNA from Salmonella enterica serovar typhimurium.

Deficiency of a modified nucleoside in tRNA often mediates suppression of +1 frameshift mutations. In Salmonella enterica serovar Typhimurium strain TR970 (hisC3737), which requires histidine for growth, a potential +1 frameshifting site, CCC-CAA-UAA, exists within the frameshifting window created by insertion of a C in the hisC gene. This site may be suppressed by peptidyl-tRNAProcmo5UGG (cmo(5)U is uridine-5-oxyacetic acid), making a frameshift when decoding the near-cognate codon CCC, provided that a pause occurs by, e.g., a slow entry of the tRNAGlnmnm5s2UUG (mnm(5)s(2)U is 5-methylaminomethyl-2-thiouridine) to the CAA codon located in the A site. We selected mutants of strain TR970 that were able to grow without histidine, and one such mutant (iscS51) was shown to have an amino acid substitution in the L-cysteine desulfurase IscS. Moreover, the levels of all five thiolated nucleosides 2-thiocytidine, mnm(5)s(2)U, 5-carboxymethylaminomethyl-2-thiouridine, 4-thiouridine, and N-6-(4-hydroxyisopentenyl)-2-methylthioadenosine present in the tRNA of S. enterica were reduced in the iscS51 mutant. In logarithmically growing cells of Escherichia coli, a deletion of the iscS gene resulted in nondetectable levels of all thiolated nucleosides in tRNA except N-6-(4-hydroxyisopentenyl)-2-methylthioadenosine, which was present at only 1.6% of the wild-type level. After prolonged incubation of cells in stationary phase, a 20% level of 2-thiocytidine and a 2% level of N-6-(4-hydroxyisopentenyl)-2-methylthioadenosine was observed, whereas no 4-thiouridine, 5-carboxymethylaminomethyl-2-thiouridine, or mnm(5)s(2)U was found. We attribute the frameshifting ability mediated by the iscS51 mutation to a slow decoding of CAA by the tRNAGlnmnm5s2UUG due to mnm(5)s(2)U deficiency. Since the growth rate of the iscS deletion mutant in rich medium was similar to that of a mutant (mnmA) lacking only mnm(5)s(2)U, we suggest that the major cause for the reduced growth rate of the iscS deletion mutant is the lack of mnm(5)s(2)U and 5-carboxymethylaminomethyl-2-thiouridine and not the lack of any of the other three thiolated nucleosides that are also absent in the iscS deletion mutant.

Carbon-Sulfur Lyases↗